The rapid emergence of breakthrough allosteric drugs, together with increasing emphasis on the molecular mechanisms of disease, underscores the critical importance of understanding biological processes at the molecular level. Among these, few concepts are as fundamental as the allosteric behavior of proteins. The importance of allostery was recognized decades ago; however, at the time proteins were viewed as static molecular structures rather than dynamic conformational ensembles that continuously interconvert among states with distinct free energies. The realization that proteins exist as dynamic conformational ensembles has transformed our understanding of oncogenic mutations, molecular recognition, protein regulation, and folding. These processes arise from the intrinsic allosteric nature of proteins embodied in their dynamic conformational ensembles. This conceptual advance has also accelerated the development of allosteric therapeutics. Here, we review the conceptual evolution of allostery from classical models to the conformational ensemble paradigm and discuss its implications for biology and modern drug discovery. We highlight breakthroughs in allosteric therapeutics, including a PROTAC that induces degradation of the Cyclin E–CDK2 complex; the pan-Ras molecular glue daraxonrasib for pancreatic cancer, whose allosteric mechanism is mediated through cyclophilin A rather than directly on Ras; a COP9 signalosome exosite-targeting agent; and other emerging modalities.
R. Nussinov, H. Jang· Journal of Molecular Biology· 0 citations
A fundamental question in cell signaling is how a single kinase, with a single primary substrate, can activate multiple distinct cellular programs. Kinases can be characterized by speed, duration, and amplitude. They should be efficient—but not necessarily maximally—as signaling functions often require slow kinetics. How the physical behavior of individual kinases, especially the top-tier kinase, coordinates the collective cascade for functional output—essential for molecular engineering and pharmacology—remains a challenge. Here we decipher the structural “why” behind the specific kinase order in cascades as the key design principle of cellular signaling, which resolves these questions. We elucidate the conformational mechanisms and catalytic actions of the sequentially ordered component kinases in seven related and distinct cascades, including MAPKs. We propose that the order of kinases in cascades is dictated by their conformational character, a mechanism amplified in cascade-enriched biomolecular condensates—establishing design principles for pathway-selective, cascade-directed therapeutics.
R. Nussinov, Clil Regev, H. Jang· RSC Chemical Biology· 0 citations
Rac2, a member of the Rho family of small GTPases, is a fundamental regulator of essential cellular processes. Pathogenic substitutions near and within the Switch II region, specifically D57N and E62K, have been implicated in oncogenesis and immunodeficiency. Despite their proximity, D57N is characterized as a loss-of-function mutation, while E62K is a constitutively active, gain-of-function mutation. In this study, we addressed several critical questions: (i) the structural basis of their altered cellular functions, (ii) how these variants rearrange the conformational ensemble, and (iii) the subsequent impact on cellular signaling networks. Using molecular dynamics (MD) simulations, we characterized the conformational dynamics of these Rac2 variants in GDP- and GTP-bound states. Our results demonstrate that Rac2D57N predominantly adopts an inactive-like conformation, regardless of the bound nucleotide. GTP binding is insufficient to induce the canonical active state in this mutant. Conversely, Rac2E62K maintains a nucleotide-dependent toggle, appearing inactive when bound to GDP and active when bound to GTP. Additionally, we examined the assembly of these variants with the regulator p50-RhoGAP. In the wild-type complex, GAP binding facilitates a shift toward a near-transition-state ensemble. In stark contrast, both the D57N and E62K complexes remain sequestered in a ground-ON state configuration, effectively trapping the GTPase and hindering GAP-mediated hydrolysis. While both Rac2 mutations result in immune system dysfunction, the underlying mechanisms are opposite: inactive vs overactive. This work provides a high-resolution, mechanistic framework for understanding how localized perturbations in the switch loops landscape dictate systemic cellular outcomes.
Single-cell breast cancer atlases reveal malignant, immune, and stromal diversity; however, how the recurrent signaling pathways drive untreated malignant-cell states and could inform combination therapy remains unclear. Here, we analyzed 15,753 malignant cells from untreated primary breast tumors using a cell-resolved network framework. Individual transcriptomes were projected onto a protein–protein interaction network, partitioned into Leiden communities, and annotated by pathway enrichment. Pathway recurrence was evaluated against matched null models preserving community size, protein-network degree, and gene detection rate. Before null correction, recurrent pathways included PI3K/AKT, MAPK, JAK/STAT, and HIF-1 (hypoxia-inducible factor 1) signaling. After correction, HIF-1 emerged as the dominant recurrent signal across patients, indicating convergence of diverse upstream pathways on a shared hypoxia- and stress-adaptive malignant-cell program. The recurrent JAK/STAT, cAMP, glucagon, oxytocin, and thyroid hormone signaling suggest inflammatory, metabolic, and endocrine crosstalk. These findings support rational drug combinations targeting HIF-1 together with upstream PI3K/AKT/mTOR, MAPK, or JAK/STAT signaling.
B. R. Yavuz, H. Jang, R. Nussinov· bioRxiv· 0 citations
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